A Novel Group of Promiscuous Podophages Infecting Diverse Gammaproteobacteria from River Communities Exhibits Dynamic Intergenus Host Adaptation

Dynamics of crAssphage as a human source tracking marker in potentially faecally polluted environments

(2019) E. Ballesté et al.   WATER RESEARCH

Integrative study of microbial community dynamics and water quality along The Apatlaco River

(2019) Luz Breton-Deval et al.   ENVIRONMENTAL POLLUTION

Phylogenetic analyses of the genus Aeromonas based on housekeeping gene sequencing and its influence on systematics

(2018) A. Navarro et al.   JOURNAL OF APPLIED MICROBIOLOGY

Molecular and Evolutionary Determinants of Bacteriophage Host Range

(2018) Patrick A. de Jonge et al.   TRENDS IN MICROBIOLOGY

Adaptation to sub-optimal hosts is a driver of viral diversification in the ocean

(2018) Hagay Enav et al.   Nature Communications

Evolutionary Genetic Analysis Uncovers Multiple Species with Distinct Habitat Preferences and Antibiotic Resistance Phenotypes in the Stenotrophomonas maltophilia Complex

(2017) Luz E. Ochoa-Sánchez et al.   Frontiers in Microbiology

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

(2016) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Isolation of Polyvalent Bacteriophages by Sequential Multiple-Host Approaches

(2015) Pingfeng Yu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Core and accessory genome architecture in a group of Pseudomonas aeruginosa Mu-like phages

(2015) Adrián Cazares et al.   BMC GENOMICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

XSEDE: Accelerating Scientific Discovery

(2014) John Towns et al.   COMPUTING IN SCIENCE & ENGINEERING

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Learning from Bacteriophages - Advantages and Limitations of Phage and Phage-Encoded Protein Applications

(2013) Zuzanna Drulis-Kawa et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Understanding Bacteriophage Specificity in Natural Microbial Communities

(2013) Britt Koskella et al.   Viruses-Basel

Complete Genome Sequence of Bacteriophage phiAS7, a T7-Like Virus That Infects Aeromonas salmonicida subsp. salmonicida

(2012) J. H. Kim et al.   JOURNAL OF VIROLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Interactive microbial genome visualization with GView

(2010) Aaron Petkau et al.   BIOINFORMATICS

The Genus Aeromonas: Taxonomy, Pathogenicity, and Infection

(2010) J. M. Janda et al.   CLINICAL MICROBIOLOGY REVIEWS

Antagonistic coevolution accelerates molecular evolution

(2010) Steve Paterson et al.   NATURE

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Prediction of whole-genome DNA G+C content within the genus Aeromonas based on housekeeping gene sequences

(2010) J. Gaspar Lorén et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

An rpoD-based PCR procedure for the identification of Pseudomonas species and for their detection in environmental samples

(2009) Magdalena Mulet et al.   MOLECULAR AND CELLULAR PROBES

phiSITE: database of gene regulation in bacteriophages

(2009) Lubos Klucar et al.   NUCLEIC ACIDS RESEARCH

Optimal Foraging by Bacteriophages through Host Avoidance

(2008) Richard H. Heineman et al.   AMERICAN NATURALIST

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Genomic Characterization of Ralstonia solanacearum Phage  RSB1, a T7-Like Wide-Host-Range Phage

(2008) T. Kawasaki et al.   JOURNAL OF BACTERIOLOGY